#change pop to HIS
 perl perl_gen_table.pl

mv filetered_r2_0_03.out HIS_filetered_r2_0_03.out
mv filetered_r2_0_08.out HIS_filetered_r2_0_08.out
#create table
perl perl_generate_table_count_snps.pl unfiletered.out HIS_filetered_r2_0_03.out HIS_filetered_r2_0_08.out > table_HIS

perl perl_filter_chn_maf.pl 10 HIS_MAF_0.02 0.02
perl perl_filter_chn_maf.pl 10 HIS_MAF_0.05 0.05
perl perl_chn_maf_filter.pl HIS_MAF_0.02 unfiletered.out unfiletered_HIS_MAF_0.02.out
perl perl_chn_maf_filter.pl HIS_MAF_0.05 unfiletered.out unfiletered_HIS_MAF_0.05.out
perl perl_chn_maf_filter.pl HIS_MAF_0.02 HIS_filetered_r2_0_03.out HIS_filetered_r2_0_03_HIS_MAF_0.02.out
perl perl_chn_maf_filter.pl HIS_MAF_0.02 HIS_filetered_r2_0_08.out HIS_filetered_r2_0_08_HIS_MAF_0.02.out
perl perl_chn_maf_filter.pl HIS_MAF_0.05 HIS_filetered_r2_0_03.out HIS_filetered_r2_0_03_HIS_MAF_0.05.out
perl perl_chn_maf_filter.pl HIS_MAF_0.05 HIS_filetered_r2_0_08.out HIS_filetered_r2_0_08_HIS_MAF_0.05.out

perl perl_generate_table_count_snps.pl unfiletered_HIS_MAF_0.02.out HIS_filetered_r2_0_03_HIS_MAF_0.02.out HIS_filetered_r2_0_08_HIS_MAF_0.02.out > table_HIS_MAF_0.02.out
perl perl_generate_table_count_snps.pl unfiletered_HIS_MAF_0.05.out HIS_filetered_r2_0_03_HIS_MAF_0.05.out HIS_filetered_r2_0_08_HIS_MAF_0.05.out > table_HIS_MAF_0.05.out
